Version 16 Add 'Features Within Selection' option to the 'Select' menu to select features that are contained by a selected base range. Saving an entry as EMBL submission has an option now to remove products from CDS features with a pseudogene qualifier. From the 'View' menu added 'Adjust panel heights...' option in ACT for adjusting their heights (BAM, VCF, plots, comparisons) by giving them different weights in order to distribute the space between each component. Added ability to hide graph lines. Right click on the graph to get the popup menu and select 'Configure...'. Then use the 'Line size' slider to reduce the size of the line(s) that you want to hide to zero. Labels can optionally be added to the header of base position plots and these are used in the legend, e.g. # colour 5:150:55 255:0:0 0:255:0 0:0:255 100:100:100 50:150:50 # label lab1 lab2 lab3 lab4 lab5 lab6 176 2204.8 848.23 0 0 0 536.04 ... In the Feature Editor there is now a button ('User Qualifiers') which opens a tool for maintaining user defined lists of qualifiers (i.e. qualifiers in the form tag = value pairs on separate lines) and the option to read qualifiers from OBO formatted files or URLs. These can be saved between sessions in the file '.artemis.qualifiers' in the home directory. Automatic addition of history qualifier in chado database mode. Added RNASeq strand specific option to the BAM popup menu ('Colour By' -> 'RNASeq Strand Specific Tag (XS)'). Reads colours are based on the XS tag (used by TopHat). The RNA strand is then used in the coverage plots and in calculation of read counts and RPKM values. Added the following flags: -Dshow_snps Show SNP marks in BamView -Dshow_snp_plot Open SNP plot in BamView -Dshow_cov_plot Open coverage plot in BamView Add validation checks. This will check the following: All file types: - CDS have no internal stop codon - CDS have valid stop codon GFF / Chado: - check complete gene model - check boundaries are valid - check all features are on the same strand - check CDS features have a phase - check attribute column - qualifiers have a value (not empty) - only reserved tags start with uppercase Validation can be run in two ways: 1. using the option in View->Feature Filters->Validation checks... which shows 'failed' features in feature list windows 2. selecting 'Validation report ...' option in the popup menu when right clicking on the feature display. This produces a report with an option to auto-fix gene boundaries and stop codons.